5 and a half hours later, all mails are in. All of them are duplicates. Upgrading Evolution apparently resets the flag to indicate which mails are new and which are not. It also involves cleaning up your inbox again. I probably missed couple of hundreds but most of the 2635 mails, were deleted.
use Net::POP3;
my $client = Net::POP3->new('mail.host.com');
$client->login('user','password');
for $mesgnum (keys %{ $client->list })
{ $client->delete($mesgnum); }
$client->quit;
